keyword
MENU ▼
Read by QxMD icon Read
search

Persistent homology

keyword
https://www.readbyqxmd.com/read/29150287/anastasis-and-the-er-stress-response-solving-the-paradox-of-the-unfolded-protein-response-in-cancer
#1
Rafael Vincent M Manalo
In recent years, studies have suggested a novel pathway for cell survival, which faces scientific skepticism and interest in its concept of cell 'resurrection' - that is, the anastasis of cells at late-stage apoptosis. While biomarkers have been discovered, many of these are related to the endoplasmic reticulum (ER) stress response - acting also to promote cell survival in the presence of perturbation. The promises of anastasis, if accepted, will greatly impact translational medicine especially in the treatment of cancer, since apoptosis is generally irreversible in the late stages, and chemotherapy is performed to maximize tumor death and minimize off-target effects...
November 2017: Medical Hypotheses
https://www.readbyqxmd.com/read/29137226/the-neglected-avian-hepatotropic-virus-induces-acute-and-chronic-hepatitis-in-ducks-an-alternative-model-for-hepatology
#2
Xumin Ou, Sai Mao, Jingyu Cao, Yunchao Ma, Guangpeng Ma, Anchun Cheng, Mingshu Wang, Dekang Zhu, Shun Chen, Renyong Jia, Mafeng Liu, Kunfeng Sun, Qiao Yang, Ying Wu, Xiaoyue Chen
Duck Hepatitis A Virus (DHAV) belongs to the Avihepatovirus, which is also classified into Picornaviridae with Hepatovirus, Hepatitis A Virus (HAV). In humans, the pathogenesis of HAV is not well understood because of limited work with animal models. Here, we investigated the progress of duck viral hepatitis caused by DHAV and their potential for dissecting the pathogenesis of HAV. During the course of infection, the duck model had undergone hepatocellular lesions (vacuolation, acidophilic degeneration and steatosis), lymphocytes recruitment (neutrophil granulocytes, heterophilic granulocytes and T cells or plasm cells) and repair (activation of hepatic stellate cells, fibrosis and regeneration)...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29123917/the-telomere-bouquet-facilitates-meiotic-prophase-progression-and-exit-in-fission-yeast
#3
Vera Moiseeva, Hanna Amelina, Laura C Collopy, Christine A Armstrong, Siân R Pearson, Kazunori Tomita
During meiotic prophase, chromosome arrangement and oscillation promote the pairing of homologous chromosomes for meiotic recombination. This dramatic movement involves clustering of telomeres at the nuclear membrane to form the so-called telomere bouquet. In fission yeast, the telomere bouquet is formed near the spindle pole body (SPB), which is the microtubule organising centre, functionally equivalent to the metazoan centrosome. Disruption of bouquet configuration impedes homologous chromosome pairing, meiotic recombination and spindle formation...
2017: Cell Discovery
https://www.readbyqxmd.com/read/29115375/persistent-stat5-mediated-ros-production-and-involvement-of-aberrant-p53-apoptotic-signaling-in-the-resistance-of-chronic-myeloid-leukemia-to-imatinib
#4
Yanhong Cheng, Yingchan Hao, Aimei Zhang, Chaojie Hu, Xiaoxiao Jiang, Quan Wu, Xiucai Xu
The persistent activation of signal transducer and activator of transcription 5 (STAT5) may principally be attributed to breakpoint cluster region (BCR)-Abelson murine leukemia viral oncogene homolog 1 (ABL1), and have multi-faceted effects in the development of chronic myeloid leukemia (CML). The p53 protein network regulates important mechanisms in DNA damage repair, cell cycle regulation/checkpoints, and cell senescence and apoptosis, as demonstrated by its ability to positively regulate the expression of various pro-apoptotic genes, including B-cell lymphoma-2 (Bcl-2) and Bcl-2-associated X protein (Bax)...
October 20, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29114052/dna-damage-response-protein-topbp1-regulates-x-chromosome-silencing-in-the-mammalian-germ-line
#5
Elias ElInati, Helen R Russell, Obah A Ojarikre, Mahesh Sangrithi, Takayuki Hirota, Dirk G de Rooij, Peter J McKinnon, James M A Turner
Meiotic synapsis and recombination between homologs permits the formation of cross-overs that are essential for generating chromosomally balanced sperm and eggs. In mammals, surveillance mechanisms eliminate meiotic cells with defective synapsis, thereby minimizing transmission of aneuploidy. One such surveillance mechanism is meiotic silencing, the inactivation of genes located on asynapsed chromosomes, via ATR-dependent serine-139 phosphorylation of histone H2AFX (γH2AFX). Stimulation of ATR activity requires direct interaction with an ATR activation domain (AAD)-containing partner...
November 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29109187/homologous-vapc-toxins-inhibit-translation-and-cell-growth-by-sequence-specific-cleavage-of-trna-fmet
#6
Lauren R Walling, J Scott Butler
Type II toxin-antitoxin (TA) systems play a critical role in the establishment and maintenance of bacterial dormancy. They are composed of a protein toxin and its cognate protein antitoxin. They function to regulate growth during conditions of stress, such as starvation or antibiotic treatment. As cellular proteases degrade the antitoxin, which normally binds and neutralizes the toxin, this frees the toxin to act on its cellular targets and arrest bacterial growth. TA systems are of particular concern in pathogenic organisms such as nontypeable Haemophilus influenzae (NTHi), as dormancy may lead to chronic infections and failure of antibiotic treatment...
November 6, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/29109182/characterization-of-an-aldolase-involved-in-cholesterol-side-chain-degradation-in-mycobacterium-tuberculosis
#7
Stephanie Gilbert, LaChae Hood, Stephen Y K Seah
The heteromeric acyl-CoA dehydrogenase, FadE28-FadE29 and the enoyl CoA hydratase ChsH1-ChsH2, encoded by genes within the intracellular growth (igr) operon of Mycobacterium tuberculosis, catalyze the dehydrogenation of the 3-carbon side chain cholesterol metabolite, 3-OPC-CoA, and subsequent hydration of the product 3-oxo-4,17-pregnadiene-20-carboxyl-CoA (3-OPDC-CoA) to form 17-hydroxy-3-oxo-4-pregnene-20-carboxyl-CoA (17-HOPC-CoA). The gene downstream of chsH2, ltp2, was expressed in recombinant Rhodococcus jostii RHA1 in combination with other genes within the igr operon...
November 6, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/29098540/multiscale-persistent-functions-for-biomolecular-structure-characterization
#8
Kelin Xia, Zhiming Li, Lin Mu
In this paper, we introduce multiscale persistent functions for biomolecular structure characterization. The essential idea is to combine our multiscale rigidity functions (MRFs) with persistent homology analysis, so as to construct a series of multiscale persistent functions, particularly multiscale persistent entropies, for structure characterization. To clarify the fundamental idea of our method, the multiscale persistent entropy (MPE) model is discussed in great detail. Mathematically, unlike the previous persistent entropy (Chintakunta et al...
November 2, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/29092799/novel-drosophila-model-for-psychiatric-disorders-including-autism-spectrum-disorder-by-targeting-of-atp-binding-cassette-protein-a
#9
Ibuki Ueoka, Hitoshi Kawashima, Atsushi Konishi, Mikio Aoki, Ryo Tanaka, Hideki Yoshida, Toru Maeda, Mamiko Ozaki, Masamitsu Yamaguchi
Autism spectrum disorder (ASD) is characterized by persistent deficits in social communication and social interactions, as well as restricted, stereotyped patterns of behavior and interests. In addition, alterations in circadian sleep-wake rhythm are common in young children with ASD. Mutations in ATP binding cassette subfamily A member 13 (ABCA13) have been recently identified in a monkey that displays behavior associated with ASD. ABCA13, a member of the ABCA family of proteins, is predicted to transport lipid molecules and is expressed in the human trachea, testis, bone marrow, hippocampus, cortex, and other tissues...
October 29, 2017: Experimental Neurology
https://www.readbyqxmd.com/read/29075860/dna-mismatch-repair-deficiency-promotes-genomic-instability-in-a-subset-of-papillary-thyroid-cancers
#10
Mahsa Javid, Thanyawat Sasanakietkul, Norman G Nicolson, Courtney E Gibson, Glenda G Callender, Reju Korah, Tobias Carling
BACKGROUND: Efficient DNA damage repair by MutL-homolog DNA mismatch repair (MMR) enzymes, MLH1, MLH3, PMS1 and PMS2, are required to maintain thyrocyte genomic integrity. We hypothesized that persistent oxidative stress and consequent transcriptional dysregulation observed in thyroid follicles will lead to MMR deficiency and potentiate papillary thyroid tumorigenesis. METHODS: MMR gene expression was analyzed by targeted microarray in 18 papillary thyroid cancer (PTC), 9 paracarcinoma normal thyroid (PCNT) and 10 normal thyroid (NT) samples...
October 11, 2017: World Journal of Surgery
https://www.readbyqxmd.com/read/29075089/exact-topological-inference-for-paired-brain-networks-via-persistent-homology
#11
Moo K Chung, Victoria Vilalta-Gil, Hyekyoung Lee, Paul J Rathouz, Benjamin B Lahey, David H Zald
We present a novel framework for characterizing paired brain networks using techniques in hyper-networks, sparse learning and persistent homology. The framework is general enough for dealing with any type of paired images such as twins, multimodal and longitudinal images. The exact nonparametric statistical inference procedure is derived on testing monotonic graph theory features that do not rely on time consuming permutation tests. The proposed method computes the exact probability in quadratic time while the permutation tests require exponential time...
June 2017: Information Processing in Medical Imaging: Proceedings of the ... Conference
https://www.readbyqxmd.com/read/29070862/persistent-homology-index-as-a-robust-quantitative-measure-of-immunohistochemical-scoring
#12
Akihiro Takiyama, Takashi Teramoto, Hiroaki Suzuki, Katsushige Yamashiro, Shinya Tanaka
Immunohistochemical data (IHC) plays an important role in clinical practice, and is typically gathered in a semi-quantitative fashion that relies on some degree of visual scoring. However, visual scoring by a pathologist is inherently subjective and manifests both intra-observer and inter-observer variability. In this study, we introduce a novel computer-aided quantification methodology for immunohistochemical scoring that uses the algebraic concept of persistent homology. Using 8 bit grayscale image data derived from 90 specimens of invasive ductal carcinoma of the breast, stained for the replicative marker Ki-67, we computed homology classes...
October 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29068165/identification-of-chlamydial-t3ss-inhibitors-through-virtual-screening-against-t3ss-atpase
#13
A V Grishin, S I Luyksaar, L N Kapotina, D D Kirsanov, E S Zayakin, A S Karyagina, N A Zigangirova
Chlamydia trachomatis is a widespread sexually transmitted pathogen that resides within a special vacuole inside host cells. Although acute infection can be treated with antibiotics, chlamydia can enter persistent state, leading to chronic infection that is difficult to cure. Thus, novel anti-chlamydial compounds active against persistent chlamydia are required. Chlamydia rely upon type III secretion system (T3SS) to inject effector proteins into host cell cytoplasm, and T3SS inhibitor are viewed as promising compounds for treatment of chlamydial infections...
October 25, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/29066623/reconciling-contradictory-findings-glucose-transporter-1-glut1-functions-as-an-oligomer-of-allosteric-alternating-access-transporters
#14
Kenneth P Lloyd, Ogooluwa A Ojelabi, Julie K De Zutter, Anthony Carruthers
Recent structural studies suggest that glucose transporter 1 (GLUT1)-mediated sugar transport is mediated by an alternating access transporter that successively presents exofacial (e2) and endofacial (e1) substrate-binding sites. Transport studies, however, indicate multiple, interacting (allosteric), and co-existent, exo- and endofacial GLUT1 ligand-binding sites. The present study asks whether these contradictory conclusions result from systematic analytical error or reveal a more fundamental relationship between transporter structure and function...
October 24, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29065857/cgdv-a-webtool-for-circular-visualization-of-genomics-and-transcriptomics-data
#15
Vineet Jha, Gulzar Singh, Shiva Kumar, Amol Sonawane, Abhay Jere, Krishanpal Anamika
BACKGROUND: Interpretation of large-scale data is very challenging and currently there is scarcity of web tools which support automated visualization of a variety of high throughput genomics and transcriptomics data and for a wide variety of model organisms along with user defined karyotypes. Circular plot provides holistic visualization of high throughput large scale data but it is very complex and challenging to generate as most of the available tools need informatics expertise to install and run them...
October 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29062589/integration-of-canonical-and-noncanonical-pathways-in-tlr4-signaling-complex-regulation-of-the-wound-repair-program
#16
REVIEW
Paula J McKeown-Longo, Paul J Higgins
Significance: Chronic inflammation and maladaptive repair contribute to the development of fibrosis that negatively impacts quality of life and organ function. The toll-like receptor (TLR) system is a critical node in the tissue response to both exogenous (pathogen-associated) and endogenous (damage-associated) molecular pattern factors (PAMPs and DAMPs, respectively). The development of novel TLR ligand-, pathway-, and/or target gene-specific therapeutics may have clinical utility in the management of the exuberant inflammatory/fibrotic tissue response to injury without compromising the host defense to pathogens...
October 1, 2017: Advances in Wound Care
https://www.readbyqxmd.com/read/29059246/macavirus-latency-associated-protein-evades-immune-detection-through-regulation-of-protein-synthesis-in-cis-depending-upon-its-glycin-glutamate-rich-domain
#17
Océane Sorel, Ting Chen, Françoise Myster, Justine Javaux, Alain Vanderplasschen, Benjamin G Dewals
Alcelaphine herpesvirus 1 (AlHV-1) is a γ-herpesvirus (γ-HV) belonging to the macavirus genus that persistently infects its natural host, the wildebeest, without inducing any clinical sign. However, cross-transmission to other ruminant species causes a deadly lymphoproliferative disease named malignant catarrhal fever (MCF). AlHV-1 ORF73 encodes the latency-associated nuclear antigen (LANA)-homolog protein (aLANA). Recently, aLANA has been shown to be essential for viral persistence in vivo and induction of MCF, suggesting that aLANA shares key properties of other γ-HV genome maintenance proteins...
October 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/29058585/preliminary-comparative-genomics-revealed-pathogenic-potential-and-international-spread-of-staphylococcus-argenteus
#18
Dao-Feng Zhang, Xiao-Yang Zhi, Jing Zhang, George C Paoli, Yan Cui, Chunlei Shi, Xianming Shi
BACKGROUND: Staphylococcus argenteus and S. schweitzeri, were recently proposed as novel species within S. aureus complex (SAC). S. argenteus has been reported in many countries and can threaten human health. S. schweitzeri has not been associated with human infections, but has been isolated from non-human primates. Questions regarding the evolution of pathogenicity of these two species will remain elusive until an exploratory evolutionary framework is established. RESULTS: We present genomic comparison analysis among members of SAC based on a pan-genome definition, which included 15 S...
October 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29058101/dock8-deficiency-presenting-as-an-ipex-like-disorder
#19
Fayhan J Alroqi, Louis-Marie Charbonnier, Sevgi Keles, Fatima Ghandour, Pierre Mouawad, Rami Sabouneh, Reem Mohammed, Abduarahman Almutairi, Janet Chou, Michel J Massaad, Raif S Geha, Zeina Baz, Talal A Chatila
PURPOSE: The dedicator of cytokinesis 8 (DOCK8) deficiency is an autosomal recessive-combined immunodeficiency whose clinical spectra include recurrent infections, autoimmunity, malignancies, elevated serum IgE, eczema, and food allergies. Here, we report on patients with loss of function DOCK8 mutations with profound immune dysregulation suggestive of an immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX)-like disorder. METHODS: Immunophenotyping of lymphocyte subpopulations and analysis of DOCK8 protein expression were evaluated by flow cytometry...
November 2017: Journal of Clinical Immunology
https://www.readbyqxmd.com/read/29054638/the-persistent-organochlorine-pesticide-endosulfan-modulates-multiple-epigenetic-regulators-with-oncogenic-potential-in-mcf-7-cells
#20
Krishna Ghosh, Biji Chatterjee, Aparna Geetha Jayaprasad, Santosh R Kanade
Environmental cues and chemicals can potentially modulate the phenotypic expression of genome through alterations in the epigenetic mechanisms. Endosulfan is one of the extensively used organochlorine pesticides around the world which is known for its endocrine, neuro- and reproductive toxicity. This study was aimed to investigate the potential of α-endosulfan in modulation of multiple epigenetic enzymes in MCF-7 cells. The cells were treated with DMSO (control) or α-endosulfan (1 and 10μM) and the expression of various epigenetic enzymes was assayed by real-time PCR and immunoblotting, in addition to their activity assays...
October 17, 2017: Science of the Total Environment
keyword
keyword
70656
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"